Soybeans (Glycine max L. Merr.) are a major cash crop and investment commodity in North America and elsewhere. Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide both in animal feed and in human food production. Additionally, soybean utilization is expanding to industrial, manufacturing, and pharmaceutical applications. Soybeans are also vulnerable to more than one hundred different pathogens, with some pathogens having disastrous economic consequences. One important soybean pathogen is the soybean aphid, which can severely impact yield. Despite a large amount of effort expended in the art, commercial soybean crops are still largely susceptible to aphid infestation.
A native of Asia, the soybean aphid (Aphis glycines Matsumura) was first found in the Midwest in 2000 (Hartman, G. L., et al., “Occurrence and distribution of Aphis glycines on soybeans in Illinois in 2000 and its potential control,” (1 Feb. 2001) Plant Management Network website). It rapidly spread throughout the region and into other parts of North America (Patterson, J. and Ragsdale, D., “Assessing and managing risk from soybean aphids in the North Central States,” (11 Apr. 2002) Soybean Research and Information Initiative website). High aphid populations can reduce crop production directly when their feeding causes severe damage such as stunting, leaf distortion, and reduced pod set (Sun, Z., et al., “Study on the uses of aphid-resistant character in wild soybean. I. Aphid-resistance performance of F2 generation from crosses between cultivated and wild soybeans,” (1990) Soybean Genet. News. 17:43-48). Yield losses attributed to the aphid in some fields in Minnesota during 2001, where several thousand aphids occurred on individual soybean plants, were >50% (Ostlie, K., “Managing soybean aphid,” (2 Oct. 2002) University of Minnesota website), with an average loss of 101 to 202 kg/ha in those fields (Patterson, J. and Ragsdale, D., “Assessing and managing risk from soybean aphids in the North Central States,” (11 Apr. 2002). In earlier reports from China, soybean yields were reduced up to 52% when there was an average of about 220 aphids per plant (Wang, X. B., et al., “A study on the damage and economic threshold of the soybean aphid at the seedling stage,” (1994) Plant Prot. (China) 20:12-13), and plant height was decreased by about 210 mm after severe aphid infestation (Wang, X. B., et al., “Study on the effects of the population dynamics of soybean aphid (Aphis glycines) on both growth and yield of soybean,” (1996) Soybean Sci. 15:243-247). An additional threat posed by the aphid is its ability to transmit certain plant viruses to soybean, such as Alfalfa mosaic virus, Soybean dwarf virus, and Soybean mosaic virus (Sama, S., et al., “Varietal screening for resistance to the aphid, Aphis glycines, in soybean,” (1974) Research Reports 1968-1974, pp. 171-172; Iwaki, M., et al., “A persistent aphid borne virus of soybean, Indonesian Soybean dwarf virus transmitted by Aphis glycines,” (1980) Plant Dis. 64:1027-1030; Hartman, G. L., et al., “Occurrence and distribution of Aphis glycines on soybeans in Illinois in 2000 and its potential control,” (1 Feb. 2001) Plant Management Network website; Hill, J. H., et al., “First report of transmission of Soybean mosaic virus and Alfalfa mosaic virus by Aphis glycines (Homoptera, Aphididae),” (1996) Appl. Entomol. 2001. 31:178-180; Clark, A. J. and Perry, K. L., “Transmissibility of field isolates of soybean viruses by Aphis glycines,” (2002) Plant Dis. 86:1219-1222).
Currently, millions of dollars are spent annually on spraying insecticides to control soybean aphid infestation. An integral component of an integrated pest management (IPM) program to control aphids is plant resistance (Auclair, J. L., “Host plant resistance,” pp. 225-265 In P. Harrewijn (ed.) Aphids: Their biology, natural enemies, and control, Vol. C., Elsevier, New York (1989); Harrewijn, P. and Minks, A. K., “Integrated aphid management: General aspects,” pp. 267-272, In A. K. Minks and P. Harrewijn (ed.) Aphids: Their biology, natural enemies, and control, Vol. C., Elsevier, New York (1989)). Insect resistance can significantly reduce input costs for producers (Luginbill, J. P., “Developing resistant plants—The ideal method of controlling insects,” (1969) USDA, ARS. Prod. Res. Rep. 111, USGPO, Washington, D.C.).
There are currently three well-documented biotypes (i.e., a subspecies of soybean aphid that shares certain genetic traits or a specified genotype) of soybean aphid that have been collected in Urbana, Ill. (biotype 1), Wooster, Ohio (biotype 2), and Indiana (biotype 3). Additionally, there are three kinds of plant resistance that have been identified: antibiosis, antixenosis, and tolerance. Antibiosis (non-choice) is the plant's ability to reduce the survival, reproduction, and fecundity of the insect. Antixenosis (choice) is the plant's ability to deter the insect from feeding or identifying the plant as a food source. Tolerance is the plant's ability to withstand heavy infestation without significant yield loss.
To date, three different soybean aphid resistance genes have been identified and mapped to the soybean genome. Rag1 was the first soybean resistance gene identified (Mian, et al., Genetic linkage mapping of the soybean aphid resistance gene in PI 243540, Theor. Appl. Genet. 117:955-962 (2008)). Rag1 has been mapped to linkage group M in the vicinity of SSR markers Satt540 and Satt463 (Kim, et al., Fine mapping of the soybean aphid resistance gene Rag1 in soybean, Theor. Appl. Genet., 120:1063-1071 (2010)). Rag2 has been mapped to linkage group F in the vicinity of SSR markers Satt334 and Sct—033 (Mian, et al., Genetic linkage mapping of the soybean aphid resistance gene in PI 243540, Theor. Appl. Genet. 117:955-962 (2008)). Rag3 is located on linkage group J in the vicinity of markers Sat—339 and Sat—370. It has also been previously determined that some aphid biotypes are resistant to certain of the Rag genes but are susceptible to others (Mian, et al., Genetic linkage mapping of the soybean aphid resistance gene in PI 243540, Theor. Appl. Genet. 117:955-962 (2008)).
Molecular markers have been used to selectively improve soybean crops through the use of marker assisted selection. Any detectible polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest. A number of soybean markers have been mapped and linkage groups created, as described in Cregan, R B., et al., “An Integrated Genetic Linkage Map of the Soybean Genome” (1999) Crop Science 39:1464-90, and more recently in Choi, et al., “A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis” (2007) Genetics 176:685-96. Many soybean markers are publicly available at the USDA affiliated soybase website (Soybase and the Soybean Breeder's Toolbox website).
Most plant traits of agronomic importance are polygenic, otherwise known as quantitative, traits. A quantitative trait is controlled by several genes located at various locations, or loci, in the plant's genome. The multiple genes have a cumulative effect which contributes to the continuous range of phenotypes observed in many plant traits. These genes are referred to as quantitative trait loci (QTL). Recombination frequency measures the extent to which a molecular marker is linked with a QTL. Lower recombination frequencies, typically measured in centiMorgans (cM), indicate greater linkage between the QTL and the molecular marker. The extent to which two features are linked is often referred to as the genetic distance. The genetic distance is also typically related to the physical distance between the marker and the QTL; however, certain biological phenomenon (including recombinational “hot spots”) can affect the relationship between physical distance and genetic distance. Generally, the usefulness of a molecular marker is determined by the genetic and physical distance between the marker and the selectable trait of interest.
In some cases, multiple closely linked markers, such as Single Nucleotide Polymorphism (SNP) markers, can be found to exist in a certain region of a plant genome encompassing one or more QTL. In such cases, by determining the allele present at each of those marker loci, a haplotype for that region of the plant genome can be determined. Further, by determining alleles or haplotypes present at multiple regions of the plant genome related to the same phenotypic trait, a marker profile for that trait can be determined. Such haplotype and marker profile information can be useful in identifying and selecting plants with certain desired traits.
There remains a need for soybean plants with improved resistance to soybean aphid and methods for identifying and selecting such plants.